Comparison of three rapid and easy bacterial DNA extraction methods for use with quantitative real-time PCR

European Journal of Clinical Microbiology and Infectious Diseases

Volumn 30, Issue 9, 2011, Pages 1053-1061

  Van Tongeren, S P ^a   Degener, J E ^a   Harmsen, H J M ^a  

^a UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; GENOMIC DNA;

ARTICLE; BACTERIAL CELL WALL; BACTERIAL COUNT; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM DETECTION; CONTROLLED STUDY; DNA BASE COMPOSITION; DNA CONTENT; DNA EXTRACTION; ESCHERICHIA COLI; INTERMETHOD COMPARISON; LABORATORY TEST; LIMIT OF QUANTITATION; NONHUMAN; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROCESS MONITORING; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; STAPHYLOCOCCUS AUREUS; VALIDATION PROCESS;

BACTERIOLOGICAL TECHNIQUES; DNA, BACTERIAL; ENVIRONMENTAL MICROBIOLOGY; ESCHERICHIA COLI; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; REAL-TIME POLYMERASE CHAIN REACTION; SPECIMEN HANDLING; STAPHYLOCOCCUS AUREUS;

EID: 80054718249     PISSN: 09349723     EISSN: 14354373     Source Type: Journal    
DOI: 10.1007/s10096-011-1191-4     Document Type: Article

References (36)

1. Zengler K, Rajilic-Stojanovic M, De Vos WM, Zoetendal EG, Sloan WT, Quince C, Curtis TP, Schmidt SK, Wilson KL, Meyer AF, Schadt CW, Porter TM, Moncalvo JM, Caron DA, Gast RJ, Fierer N, Rosselló-Mora R, López-López A, Fuhrman JA, Nelson KE, Janssen PH, Ciche TA, Kartal B, Strous M, Avery SV, Desikan R, Tetard L, Passian A, Datar RH, Thundat T, Keller M, Schadt CW, Palumbo AV, Smith HO, Glass JI, Hutchison CA 3rd, Venter JC (2008) Accessing uncultivated microorganisms: From the environment to organisms and genomes and back. ASM Press, Washington, DC
2. van Tongeren SP, Krooneman J, Raangs GC, Welling GW, Harmsen HJM (2007) Microbial detection and monitoring in advanced life support systems like the International Space Station. Microgravity Sci Technol 19:45-48 (Pubitemid 47114352)
3. Espy MJ, Uhl JR, Sloan LM, Buckwalter SP, Jones MF, Vetter EA, Yao JD, Wengenack NL, Rosenblatt JE, Cockerill FR 3rd, Smith TF (2006) Real-time PCR in clinical microbiology: Applications for routine laboratory testing. Clin Microbiol Rev 19:165-256 (Pubitemid 43158452)
4. Bastien P, Procop GW, Reischl U (2008) Quantitative real-time PCR is not more sensitive than "conventional" PCR. J Clin Microbiol 46:1897-1900 (Pubitemid 351831816)
5. Cook KL, Britt JS (2007) Optimization of methods for detecting Mycobacterium avium subsp. paratuberculosis in environmental samples using quantitative, real-time PCR. J Microbiol Methods 69:154-160 (Pubitemid 46427936)
6. Rantakokko-Jalava K, Jalava J (2002) Optimal DNA isolation method for detection of bacteria in clinical specimens by broadrange PCR. J Clin Microbiol 40:4211-4217 (Pubitemid 35285815)
7. Ludwig W, Schleifer KH (2000) How quantitative is quantitative PCR with respect to cell counts? Syst Appl Microbiol 23:556-562 (Pubitemid 32110947)
8. Coyne SR, Craw PD, Norwood DA, Ulrich MP (2004) Comparative analysis of the Schleicher and Schuell IsoCode Stix DNA isolation device and the Qiagen QIAamp DNA Mini Kit. J Clin Microbiol 42:4859-4862 (Pubitemid 39362425)
9. Reischl U, Linde HJ, Metz M, Leppmeier B, Lehn N (2000) Rapid identification of methicillin-resistant Staphylococcus aureus and simultaneous species confirmation using real-time fluorescence PCR. J Clin Microbiol 38:2429-2433 (Pubitemid 30414386)
10. Harmsen HJM, Raangs GC, He T, Degener JE, Welling GW (2002) Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Appl Environ Microbiol 68:2982-2990 (Pubitemid 34602022)
11. Brasher CW, DePaola A, Jones DD, Bej AK (1998) Detection of microbial pathogens in shellfish with multiplex PCR. Curr Microbiol 37:101-107 (Pubitemid 28337655)
12. Hogg GM,McKenna JP, Ong G (2008) Rapid detection ofmethicillinsusceptible and methicillin-resistant Staphylococcus aureus directly from positive BacT/Alert® blood culture bottles using real-time polymerase chain reaction: Evaluation and comparison of 4 DNA extraction methods. Diagn Microbiol Infect Dis 61:446-452 (Pubitemid 351970646)
13. Cremonesi P, Castiglioni B, Malferrari G, Biunno I, Vimercati C, Moroni P, Morandi S, Luzzana M (2006) Technical note: Improved method for rapid DNA extraction of mastitis pathogens directly from milk. J Dairy Sci 89:163-169 (Pubitemid 43105920)
14. Cenci-Goga BT, Crotti S, Costarelli S, Rondini C, Karama M, Bennett P (2004) Detection of tet(M) gene from raw milk by rapid DNA extraction followed by a two-step PCR with nested primers. J Food Prot 67:2833-2838 (Pubitemid 39623369)
15. Gullsby K, Hallander HO, Bondeson K (2007) Performance of Bordetella pertussis IS481 real-time PCR in a vaccine trial setting. APMIS 115:1370-1375
16. AldousWK, Pounder JI, Cloud JL,Woods GL (2005) Comparison of six methods of extracting Mycobacterium tuberculosis DNA from processed sputum for testing by quantitative real-time PCR. J Clin Microbiol 43:2471-2473 (Pubitemid 40656270)
17. Lee SH, Jung BY, Rayamahji N, Lee HS, Jeon WJ, Choi KS, Kweon CH, Yoo HS (2009) A multiplex real-time PCR for differential detection and quantification of Salmonella spp., Salmonella enterica serovar Typhimurium and Enteritidis in meats. J Vet Sci 10:43-51
18. Luan C, Levin RE (2008) Use of activated carbon coated with bentonite for increasing the sensitivity of pcr detection of Escherichia coli O157:H7 in Canadian oyster (Crassostrea gigas) tissue. J Microbiol Methods 72:67-72 (Pubitemid 350309687)
19. Wilson DA, Yen-Lieberman B, Reischl U, Gordon SM, Procop GW (2003) Detection of Legionella pneumophila by real-time PCR for the mip gene. J Clin Microbiol 41:3327-3330 (Pubitemid 36842342)
20. Wilson D, Yen-Lieberman B, Reischl U, Warshawsky I, Procop GW (2004) Comparison of five methods for extraction of Legionella pneumophila from respiratory specimens. J Clin Microbiol 42:5913-5916 (Pubitemid 39664393)
21. Peters RPH, van Agtmael MA, Gierveld S, Danner SA, Groeneveld ABJ, Vandenbroucke-Grauls CMJE, Savelkoul PHM (2007) Quantitative detection of Staphylococcus aureus and Enterococcus faecalis DNA in blood to diagnose bacteremia in patients in the intensive care unit. J Clin Microbiol 45:3641-3646 (Pubitemid 350156861)
22. Morio F, Corvec S, Caroff N, Le Gallou F, Drugeon H, Reynaud A (2008) Real-time PCR assay for the detection and quantification of Legionella pneumophila in environmental water samples: Utility for daily practice. Int J Hyg Environ Health 211:403-411 (Pubitemid 351847840)
23. Simms I, Eastick K, Mallinson H, Thomas K, Gokhale R, Hay P, Herring A, Rogers PA (2003) Associations between Mycoplasma genitalium, Chlamydia trachomatis, and pelvic inflammatory disease. Sex Transm Infect 79:154-156 (Pubitemid 36469624)
24. Dauphin LA, Stephens KW, Eufinger SC, Bowen MD (2010) Comparison of five commercial DNA extraction kits for the recovery of Yersinia pestis DNA from bacterial suspensions and spiked environmental samples. J Appl Microbiol 108:163-172
25. Rajendram D, Ayenza R, Holder FM, Moran B, Long T, Shah HN (2006) Long-term storage and safe retrieval of DNA from microorganisms for molecular analysis using FTA matrix cards. J Microbiol Methods 67:582-592 (Pubitemid 44633478)
26. Jaravata CV, Smith WL, Rensen GJ, Ruzante JM, Cullor JS (2006) Detection of Mycobacterium avium subsp. paratuberculosis in bovine manure using Whatman FTA card technology and Lightcycler real-time PCR. Foodborne Pathog Dis 3:212-215 (Pubitemid 43887060)
27. Nechvatal JM, Ram JL, Basson MD, Namprachan P, Niec SR, Badsha KZ, Matherly LH, Majumdar APN, Kato I (2008) Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces. J Microbiol Methods 72:124-132
28. Reischl U, Pulz M, Ehret W, Wolf H (1994) PCR-based detection of mycobacteria in sputum samples using a simple and reliable DNA extraction protocol. Biotechniques 17:844-845 (Pubitemid 24345996)
29. Miller MB, Meyer H, Rogers E, Gilligan PH (2005) Comparison of conventional susceptibility testing, penicillin-binding protein 2a latex agglutination testing, and mecA real-time PCR for detection of oxacillin resistance in Staphylococcus aureus and coagulasenegative Staphylococcus. J Clin Microbiol 43:3450-3452 (Pubitemid 40981363)
30. Sakai H, Procop GW, Kobayashi N, Togawa D, Wilson DA, Borden L, Krebs V, Bauer TW (2004) Simultaneous detection of Staphylococcus aureus and coagulase-negative staphylococci in positive blood cultures by real-time PCR with two fluorescence resonance energy transfer probe sets. J Clin Microbiol 42:5739-5744 (Pubitemid 39664361)
31. Shrestha NK, Tuohy MJ, Padmanabhan RA, Hall GS, Procop GW (2005) Evaluation of the LightCycler Staphylococcus MGRADE kits on positive blood cultures that contained gram-positive cocci in clusters. J Clin Microbiol 43:6144-6146 (Pubitemid 43100677)
32. Shrestha NK, Tuohy MJ, Hall GS, Reischl U, Gordon SM, Procop GW (2003) Detection and differentiation of Mycobacterium tuberculosis and nontuberculous mycobacterial isolates by realtime PCR. J Clin Microbiol 41:5121-5126 (Pubitemid 37429925)
33. Shrestha NK, Tuohy MJ, Hall GS, Isada CM, Procop GW (2002) Rapid identification of Staphylococcus aureus and the mecA gene from BacT/ALERT blood culture bottles by using the LightCycler system. J Clin Microbiol 40:2659-2661 (Pubitemid 34747384)
34. Zucol F, Ammann RA, Berger C, Aebi C, Altwegg M, Niggli FK, Nadal D (2006) Real-time quantitative broad-range PCR assay for detection of the 16S rRNA gene followed by sequencing for species identification. J Clin Microbiol 44:2750-2759 (Pubitemid 44228567)
35. Pierson DL (2001) Microbial contamination of spacecraft. Gravit Space Biol Bull 14:1-6
36. Fredricks DN, Smith C, Meier A (2005) Comparison of six DNA extraction methods for recovery of fungal DNA as assessed by quantitative PCR. J Clin Microbiol 43:5122-5128 (Pubitemid 41484015)